It was built in 1889 as a passenger station and freight warehouse for the Seattle, Lake Shore and Eastern Railway (SLS&E),[2] serving what was then known as Gilman, Washington (and as Squak Valley until 1888).

Only a few years after the depot's opening, in the 1890s, the SLS&E was taken over by the Northern Pacific Railway.

[2] The Issaquah Depot's use as a passenger station ended in the 1940s, and Northern Pacific abandoned the building in 1962.

[2] Restoration began in 1985[3] and was completed in the early 1990s, and the depot now operates as a museum, managed by the non-profit Issaquah Historical Museums (formerly known as the Issaquah Historical Society).

The building was added to the National Register of Historic Places in 1990.